HEADER    DNA                                     13-OCT-99   1D6D              
TITLE     SOLUTION DNA STRUCTURE CONTAINING (A-A)-T TRIADS INTERDIGITATED       
TITLE    2 BETWEEN A-T BASE PAIRS AND GGGG TETRADS; NMR, 8 STRUCT.              
COMPND    MOL_ID: 1;                                                            
COMPND   2 MOLECULE: 5'-D(*AP*AP*GP*GP*TP*TP*TP*TP*AP*AP*GP*G)-3';              
COMPND   3 CHAIN: A, B;                                                         
COMPND   4 ENGINEERED: YES                                                      
SOURCE    MOL_ID: 1;                                                            
SOURCE   2 SYNTHETIC: YES;                                                      
SOURCE   3 OTHER_DETAILS: THIS SEQUENCE OCCURS NATURALLY IN HUMAN TELOMERIC     
SOURCE   4 DNA, HUMAN IG SUPERFAMILY CYTOTOXIC T-LYMPHOCYTE-ASSOCIATED PROTEIN  
SOURCE   5 GENE AND 16S RRNA OF HENRICA NIPONICA.                               
KEYWDS    MULTI-STRANDED DNA ARCHITECTURE, G-TETRAD, T-(A-A) TRIAD, A(SYN)-     
KEYWDS   2 A(ANTI) PLATFORM, ZIPPER MOTIF, BASE-SUGAR STACKING, DNA             
EXPDTA    SOLUTION NMR                                                          
NUMMDL    8                                                                     
AUTHOR    V.V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL                       
REVDAT   6   22-MAY-24 1D6D    1       REMARK                                   
REVDAT   5   16-FEB-22 1D6D    1       REMARK                                   
REVDAT   4   24-FEB-09 1D6D    1       VERSN                                    
REVDAT   3   01-APR-03 1D6D    1       JRNL                                     
REVDAT   2   03-FEB-00 1D6D    1       JRNL                                     
REVDAT   1   17-JAN-00 1D6D    0                                                
JRNL        AUTH   V.KURYAVYI,A.KETTANI,W.WANG,R.JONES,D.J.PATEL                
JRNL        TITL   A DIAMOND-SHAPED ZIPPER-LIKE DNA ARCHITECTURE CONTAINING     
JRNL        TITL 2 TRIADS SANDWICHED BETWEEN MISMATCHES AND TETRADS.            
JRNL        REF    J.MOL.BIOL.                   V. 295   455 2000              
JRNL        REFN                   ISSN 0022-2836                               
JRNL        PMID   10623538                                                     
JRNL        DOI    10.1006/JMBI.1999.3345                                       
REMARK   2                                                                      
REMARK   2 RESOLUTION. NOT APPLICABLE.                                          
REMARK   3                                                                      
REMARK   3 REFINEMENT.                                                          
REMARK   3   PROGRAM     : X-PLOR 3.1                                           
REMARK   3   AUTHORS     : A.BRUNGER                                            
REMARK   3                                                                      
REMARK   3  OTHER REFINEMENT REMARKS: A TOTAL OF 100 INITIAL DNA STRUCTURES     
REMARK   3  WERE GENERATED USING THE METRIC MATRIX DISTANCE GEOMETRY            
REMARK   3  PROTOCOL OF X-PLOR WITH THE DISTANCE RESTRAINTS OBTAINED            
REMARK   3  EXPERIMENTALLY SPECIFIED AS NOE WITH THE "SUM" AVERAGING            
REMARK   3  OPTION.TEN BEST STRUCTURES SELECTED ON THE BASIS OF GOOD            
REMARK   3  COVALENT GEOMETRY, LOW DISTANCE RESTRAINT VIOLATION AND             
REMARK   3  FAVOURABLE NON-BONDED ENERGY WERE FURTHER OPTIMIZED WITH            
REMARK   3  RESTRAINED MOLECULAR DYNAMICS, MOLECULAR MECHANICS AND              
REMARK   3  RELAXATION MATRIX INTENSITY REFINEMENT.THE PROTOCOLS ARE AS         
REMARK   3  FOLLOWS. THE DYNAMICS WAS INITIATED AT 300K AND THE TEMPERATURE     
REMARK   3  WAS INCREASED TO 1000K DURING 7PS. AFTER 0.5 PS THE FORCE           
REMARK   3  CONSTANTS WERE GRADUALLY SCALED DURING 17.5 PSEC IN THE             
REMARK   3  PROPORTION 1: 4:8 FOR THREE CLASSES OF NOE: EXCHANGEABLE,           
REMARK   3  NONEXCHANGEABLE AND HYDROGEN BONDS, RESP. THE STRUCTURES WERE       
REMARK   3  THEN SLOWLY COOLED TO 300K IN 2.8 PS AND EQUILIBRATED AT 300K       
REMARK   3  FOR 12 PS. THE COORDINATES SAVED EVERY 0.5 PS DURING THE LAST       
REMARK   3  4.0 PS WERE AVERAGED AND THE AVERAGE STRUCTURE WAS SUBJECTED TO     
REMARK   3  3000 STEPS OF MINIMIZATION. THE HYDROGEN BONDS OF THE GGGG          
REMARK   3  TETRADS, AND NON- CRYSTALLOGRAPHIC SYMMETRY RESTRAINTS WERE         
REMARK   3  MAINTAINED THROUGHOUT. THE OBTAINED STRUCTURES WERE SUBJECTED TO    
REMARK   3  RELAXATION MATRIX INTENSITY REFINEMENT. THE INTENSIY VOLUMES        
REMARK   3  WERE USED AS RESTRAINTS. THE RELAXATION PATHWAYS WERE CALCULATED    
REMARK   3  USING CUTOFF 4.5 ANGSTROM AND 7.25 NS ISOTROPIC CORRELATION         
REMARK   3  TIME. THE STRUCTURES EXHIBIT PAIRWISE R.M.S.D. VALUE OF 1.16 A.     
REMARK   3  IN TWO STRUCTURES THE RESIDUES T6 AND T8 DEVIATE FROM TWO           
REMARK   3  CLUSTERS FORMED BY REST OF 8 STRUCTURES, AND THESE TWO              
REMARK   3  STRUCTURES WERE OMITTED FROM DEPOSITION.                            
REMARK   4                                                                      
REMARK   4 1D6D COMPLIES WITH FORMAT V. 3.15, 01-DEC-08                         
REMARK 100                                                                      
REMARK 100 THIS ENTRY HAS BEEN PROCESSED BY RCSB ON 14-OCT-99.                  
REMARK 100 THE DEPOSITION ID IS D_1000009829.                                   
REMARK 210                                                                      
REMARK 210 EXPERIMENTAL DETAILS                                                 
REMARK 210  EXPERIMENT TYPE                : NMR                                
REMARK 210  TEMPERATURE           (KELVIN) : 278                                
REMARK 210  PH                             : 6.9                                
REMARK 210  IONIC STRENGTH                 : 150MM NACL                         
REMARK 210  PRESSURE                       : 1 ATM                              
REMARK 210  SAMPLE CONTENTS                : 5-10 MM DNA (SINGLE STRANDS);      
REMARK 210                                   5MM SODIUM PHOSPHATE BUFFER; 5-    
REMARK 210                                   10 MM DNA (SINGLE STRANDS); 5MM    
REMARK 210                                   SODIUM PHOSPHATE BUFFER; 5-10 MM   
REMARK 210                                   DNA (SINGLE STRANDS); 5MM SODIUM   
REMARK 210                                   PHOSPHATE BUFFER;SINGLE BASE       
REMARK 210                                   SUBSTITUTED FOR 8-BRDG, 8-BRDA,    
REMARK 210                                   DU, 5BRDU OR 2,6DA.; 5-10 MM DNA   
REMARK 210                                   (SINGLE STRANDS); 5MM SODIUM       
REMARK 210                                   PHOSPHATE BUFFER;SINGLE BASE       
REMARK 210                                   SUBSTITUTED FOR 8-BRDG, 8-BRDA,    
REMARK 210                                   DU, 5BRDU OR 2,6DA.                
REMARK 210                                                                      
REMARK 210  NMR EXPERIMENTS CONDUCTED      : NOESY; TOCSY; DQF-COSY; COSY-45;   
REMARK 210                                   1H-31P COSY ON ORIGINAL AND SITE-  
REMARK 210                                   SPECIFIC SUBSTITUTED SAMPLES       
REMARK 210                                   CONTAINING 8BR-A, 8BR-G,DU,5BR-    
REMARK 210                                   DU,2,6-DA ANALOGS.                 
REMARK 210  SPECTROMETER FIELD STRENGTH    : 600 MHZ                            
REMARK 210  SPECTROMETER MODEL             : VARIAN UNITY INOVA                 
REMARK 210  SPECTROMETER MANUFACTURER      : VARIAN                             
REMARK 210                                                                      
REMARK 210  STRUCTURE DETERMINATION.                                            
REMARK 210   SOFTWARE USED                 : VNMR 5.0, FELIX 97.0, X-PLOR 3.1   
REMARK 210   METHOD USED                   : DISTANCE GEOMETRY AND SIMULATED    
REMARK 210                                   ANNEALING, DISTANCE RESTRAINED     
REMARK 210                                   MOLECULAR DYNAMICS REFINEMENT      
REMARK 210                                   AND RELAXATION MATRIX INTENSITY    
REMARK 210                                   REFINEMENT                         
REMARK 210                                                                      
REMARK 210 CONFORMERS, NUMBER CALCULATED   : 100                                
REMARK 210 CONFORMERS, NUMBER SUBMITTED    : 8                                  
REMARK 210 CONFORMERS, SELECTION CRITERIA  : BACK CALCULATED DATA AGREE WITH    
REMARK 210                                   EXPERIMENTAL NOESY SPECTRUM,       
REMARK 210                                   STRUCTURES WITH ACCEPTABLE         
REMARK 210                                   COVALENT GEOMETRY,STRUCTURES       
REMARK 210                                   WITH FAVORABLE NON-BOND ENERGY,    
REMARK 210                                   STRUCTURES WITH THE LEAST          
REMARK 210                                   RESTRAINT VIOLATIONS,STRUCTURES    
REMARK 210                                   WITH THE LOWEST ENERGY             
REMARK 210                                                                      
REMARK 210 BEST REPRESENTATIVE CONFORMER IN THIS ENSEMBLE : 3                   
REMARK 210                                                                      
REMARK 210 REMARK: NULL                                                         
REMARK 215                                                                      
REMARK 215 NMR STUDY                                                            
REMARK 215 THE COORDINATES IN THIS ENTRY WERE GENERATED FROM SOLUTION           
REMARK 215 NMR DATA.  PROTEIN DATA BANK CONVENTIONS REQUIRE THAT                
REMARK 215 CRYST1 AND SCALE RECORDS BE INCLUDED, BUT THE VALUES ON              
REMARK 215 THESE RECORDS ARE MEANINGLESS.                                       
REMARK 300                                                                      
REMARK 300 BIOMOLECULE: 1                                                       
REMARK 300 SEE REMARK 350 FOR THE AUTHOR PROVIDED AND/OR PROGRAM                
REMARK 300 GENERATED ASSEMBLY INFORMATION FOR THE STRUCTURE IN                  
REMARK 300 THIS ENTRY. THE REMARK MAY ALSO PROVIDE INFORMATION ON               
REMARK 300 BURIED SURFACE AREA.                                                 
REMARK 350                                                                      
REMARK 350 COORDINATES FOR A COMPLETE MULTIMER REPRESENTING THE KNOWN           
REMARK 350 BIOLOGICALLY SIGNIFICANT OLIGOMERIZATION STATE OF THE                
REMARK 350 MOLECULE CAN BE GENERATED BY APPLYING BIOMT TRANSFORMATIONS          
REMARK 350 GIVEN BELOW.  BOTH NON-CRYSTALLOGRAPHIC AND                          
REMARK 350 CRYSTALLOGRAPHIC OPERATIONS ARE GIVEN.                               
REMARK 350                                                                      
REMARK 350 BIOMOLECULE: 1                                                       
REMARK 350 AUTHOR DETERMINED BIOLOGICAL UNIT: DIMERIC                           
REMARK 350 APPLY THE FOLLOWING TO CHAINS: A, B                                  
REMARK 350   BIOMT1   1  1.000000  0.000000  0.000000        0.00000            
REMARK 350   BIOMT2   1  0.000000  1.000000  0.000000        0.00000            
REMARK 350   BIOMT3   1  0.000000  0.000000  1.000000        0.00000            
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: CLOSE CONTACTS                                             
REMARK 500                                                                      
REMARK 500 THE FOLLOWING ATOMS ARE IN CLOSE CONTACT.                            
REMARK 500                                                                      
REMARK 500  ATM1  RES C  SSEQI   ATM2  RES C  SSEQI           DISTANCE          
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND LENGTHS                                      
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,2(A3,1X,A1,I4,A1,1X,A4,3X),1X,F6.3)               
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   RES CSSEQI ATM2   DEVIATION                     
REMARK 500  1  DA A  10   C5'    DA A  10   C4'     0.045                       
REMARK 500  1  DA B  10   C5'    DA B  10   C4'     0.045                       
REMARK 500  2  DA A  10   C5'    DA A  10   C4'     0.048                       
REMARK 500  2  DA B  10   C5'    DA B  10   C4'     0.048                       
REMARK 500  3  DA A  10   C5'    DA A  10   C4'     0.042                       
REMARK 500  4  DA A  10   C5'    DA A  10   C4'     0.045                       
REMARK 500  4  DA B  10   C5'    DA B  10   C4'     0.046                       
REMARK 500  5  DA A  10   C5'    DA A  10   C4'     0.050                       
REMARK 500  5  DA B  10   C5'    DA B  10   C4'     0.050                       
REMARK 500  6  DA A  10   C5'    DA A  10   C4'     0.042                       
REMARK 500  6  DA B  10   C5'    DA B  10   C4'     0.042                       
REMARK 500  8  DA A  10   C5'    DA A  10   C4'     0.054                       
REMARK 500  8  DA B  10   C5'    DA B  10   C4'     0.054                       
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
REMARK 500                                                                      
REMARK 500 GEOMETRY AND STEREOCHEMISTRY                                         
REMARK 500 SUBTOPIC: COVALENT BOND ANGLES                                       
REMARK 500                                                                      
REMARK 500 THE STEREOCHEMICAL PARAMETERS OF THE FOLLOWING RESIDUES              
REMARK 500 HAVE VALUES WHICH DEVIATE FROM EXPECTED VALUES BY MORE               
REMARK 500 THAN 6*RMSD (M=MODEL NUMBER; RES=RESIDUE NAME; C=CHAIN               
REMARK 500 IDENTIFIER; SSEQ=SEQUENCE NUMBER; I=INSERTION CODE).                 
REMARK 500                                                                      
REMARK 500 STANDARD TABLE:                                                      
REMARK 500 FORMAT: (10X,I3,1X,A3,1X,A1,I4,A1,3(1X,A4,2X),12X,F5.1)              
REMARK 500                                                                      
REMARK 500 EXPECTED VALUES PROTEIN: ENGH AND HUBER, 1999                        
REMARK 500 EXPECTED VALUES NUCLEIC ACID: CLOWNEY ET AL 1996                     
REMARK 500                                                                      
REMARK 500  M RES CSSEQI ATM1   ATM2   ATM3                                     
REMARK 500  1  DA A   1   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500  1  DA A   1   N7  -  C8  -  N9  ANGL. DEV. =   4.2 DEGREES          
REMARK 500  1  DA A   2   O4' -  C1' -  N9  ANGL. DEV. =   3.3 DEGREES          
REMARK 500  1  DA A   2   N7  -  C8  -  N9  ANGL. DEV. =   3.5 DEGREES          
REMARK 500  1  DG A   3   O4' -  C1' -  N9  ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1  DG A   3   N7  -  C8  -  N9  ANGL. DEV. =   4.6 DEGREES          
REMARK 500  1  DG A   3   C8  -  N9  -  C4  ANGL. DEV. =  -2.5 DEGREES          
REMARK 500  1  DG A   4   O4' -  C1' -  N9  ANGL. DEV. =   3.8 DEGREES          
REMARK 500  1  DG A   4   N7  -  C8  -  N9  ANGL. DEV. =   4.8 DEGREES          
REMARK 500  1  DG A   4   C8  -  N9  -  C4  ANGL. DEV. =  -2.6 DEGREES          
REMARK 500  1  DT A   5   O4' -  C1' -  N1  ANGL. DEV. =   3.1 DEGREES          
REMARK 500  1  DT A   6   O4' -  C1' -  N1  ANGL. DEV. =   3.0 DEGREES          
REMARK 500  1  DT A   7   O4' -  C1' -  N1  ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1  DT A   8   O4' -  C1' -  N1  ANGL. DEV. =   3.3 DEGREES          
REMARK 500  1  DA A   9   O4' -  C1' -  N9  ANGL. DEV. =   3.0 DEGREES          
REMARK 500  1  DA A   9   N7  -  C8  -  N9  ANGL. DEV. =   4.0 DEGREES          
REMARK 500  1  DA A  10   O4' -  C1' -  N9  ANGL. DEV. =   2.8 DEGREES          
REMARK 500  1  DA A  10   N7  -  C8  -  N9  ANGL. DEV. =   4.0 DEGREES          
REMARK 500  1  DG A  11   O4' -  C1' -  N9  ANGL. DEV. =   3.8 DEGREES          
REMARK 500  1  DG A  11   N7  -  C8  -  N9  ANGL. DEV. =   4.8 DEGREES          
REMARK 500  1  DG A  11   C8  -  N9  -  C4  ANGL. DEV. =  -2.4 DEGREES          
REMARK 500  1  DG A  12   O4' -  C1' -  N9  ANGL. DEV. =   2.2 DEGREES          
REMARK 500  1  DG A  12   N7  -  C8  -  N9  ANGL. DEV. =   4.6 DEGREES          
REMARK 500  1  DG A  12   C8  -  N9  -  C4  ANGL. DEV. =  -2.8 DEGREES          
REMARK 500  1  DA B   1   O4' -  C1' -  N9  ANGL. DEV. =   2.9 DEGREES          
REMARK 500  1  DA B   1   N7  -  C8  -  N9  ANGL. DEV. =   4.2 DEGREES          
REMARK 500  1  DA B   2   O4' -  C1' -  N9  ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1  DA B   2   N7  -  C8  -  N9  ANGL. DEV. =   3.5 DEGREES          
REMARK 500  1  DG B   3   O4' -  C1' -  N9  ANGL. DEV. =   3.3 DEGREES          
REMARK 500  1  DG B   3   N7  -  C8  -  N9  ANGL. DEV. =   4.5 DEGREES          
REMARK 500  1  DG B   3   C8  -  N9  -  C4  ANGL. DEV. =  -2.5 DEGREES          
REMARK 500  1  DG B   4   O4' -  C1' -  N9  ANGL. DEV. =   3.9 DEGREES          
REMARK 500  1  DG B   4   N7  -  C8  -  N9  ANGL. DEV. =   4.8 DEGREES          
REMARK 500  1  DG B   4   C8  -  N9  -  C4  ANGL. DEV. =  -2.7 DEGREES          
REMARK 500  1  DT B   5   O4' -  C1' -  N1  ANGL. DEV. =   3.1 DEGREES          
REMARK 500  1  DT B   6   O4' -  C1' -  N1  ANGL. DEV. =   3.0 DEGREES          
REMARK 500  1  DT B   7   O4' -  C1' -  N1  ANGL. DEV. =   3.4 DEGREES          
REMARK 500  1  DT B   8   O4' -  C1' -  N1  ANGL. DEV. =   3.3 DEGREES          
REMARK 500  1  DA B   9   O4' -  C1' -  N9  ANGL. DEV. =   3.0 DEGREES          
REMARK 500  1  DA B   9   N7  -  C8  -  N9  ANGL. DEV. =   3.9 DEGREES          
REMARK 500  1  DA B  10   O4' -  C1' -  N9  ANGL. DEV. =   2.8 DEGREES          
REMARK 500  1  DA B  10   N7  -  C8  -  N9  ANGL. DEV. =   4.1 DEGREES          
REMARK 500  1  DG B  11   O4' -  C1' -  N9  ANGL. DEV. =   3.8 DEGREES          
REMARK 500  1  DG B  11   N7  -  C8  -  N9  ANGL. DEV. =   4.8 DEGREES          
REMARK 500  1  DG B  11   C8  -  N9  -  C4  ANGL. DEV. =  -2.4 DEGREES          
REMARK 500  1  DG B  12   O4' -  C1' -  N9  ANGL. DEV. =   2.2 DEGREES          
REMARK 500  1  DG B  12   N7  -  C8  -  N9  ANGL. DEV. =   4.7 DEGREES          
REMARK 500  1  DG B  12   C8  -  N9  -  C4  ANGL. DEV. =  -2.9 DEGREES          
REMARK 500  2  DA A   1   O4' -  C1' -  N9  ANGL. DEV. =   3.5 DEGREES          
REMARK 500  2  DA A   1   N7  -  C8  -  N9  ANGL. DEV. =   4.1 DEGREES          
REMARK 500                                                                      
REMARK 500 THIS ENTRY HAS     386 ANGLE DEVIATIONS.                             
REMARK 500                                                                      
REMARK 500 REMARK: NULL                                                         
DBREF  1D6D A    1    12  PDB    1D6D     1D6D             1     12             
DBREF  1D6D B    1    12  PDB    1D6D     1D6D             1     12             
SEQRES   1 A   12   DA  DA  DG  DG  DT  DT  DT  DT  DA  DA  DG  DG              
SEQRES   1 B   12   DA  DA  DG  DG  DT  DT  DT  DT  DA  DA  DG  DG              
CRYST1    1.000    1.000    1.000  90.00  90.00  90.00 P 1           1          
ORIGX1      1.000000  0.000000  0.000000        0.00000                         
ORIGX2      0.000000  1.000000  0.000000        0.00000                         
ORIGX3      0.000000  0.000000  1.000000        0.00000                         
SCALE1      1.000000  0.000000  0.000000        0.00000                         
SCALE2      0.000000  1.000000  0.000000        0.00000                         
SCALE3      0.000000  0.000000  1.000000        0.00000                         
MODEL        1